Run JSGME in your SH4 install folder and click "Tasks...", then click "Generate snapshot of game files". This will help if you experience any corruption issues later, and create a subfolder called "MODS" in your SH4 directory. Extract the FOTRSU archive into this folder, then run JSGME. You should now be able to install the mod.
General notes:
Make sure you haven't installed SH4 into the Program Files folders in Windows 8 or 10, and maybe 7.
Make sure you're installing the mod into an unmodded version of SH4.
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